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Detailed information for vg0139276484:

Variant ID: vg0139276484 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 39276484
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 340. )

Flanking Sequence (100 bp) in Reference Genome:


TTGTTGAACCAAAGGAAAAACATGGGTTATTCGTGGATATCTTTTACCTTCACCTAGGACAAGAACAAGGTCACTGTCAATCACAGTAGGAATCCTATGT[G/A,T]
CAATTGTAATAACTGTGCAATTGTTTGTCTCTTGCCTTATAGTCTTTTGGATGATATTATCTGTTGCGGTATCAACCGATGCTGTGGCTTCATCCAGAAC

Reverse complement sequence

GTTCTGGATGAAGCCACAGCATCGGTTGATACCGCAACAGATAATATCATCCAAAAGACTATAAGGCAAGAGACAAACAATTGCACAGTTATTACAATTG[C/T,A]
ACATAGGATTCCTACTGTGATTGACAGTGACCTTGTTCTTGTCCTAGGTGAAGGTAAAAGATATCCACGAATAACCCATGTTTTTCCTTTGGTTCAACAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.00% 0.60% 0.40% 0.00% T: 0.02%
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 96.80% 1.90% 1.26% 0.00% T: 0.07%
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 95.40% 2.90% 1.69% 0.00% NA
Tropical Japonica  504 99.40% 0.00% 0.40% 0.00% T: 0.20%
Japonica Intermediate  241 95.90% 2.50% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0139276484 G -> T LOC_Os01g67580.1 missense_variant ; p.Ala1337Glu; MODERATE nonsynonymous_codon ; A1337E Average:58.831; most accessible tissue: Minghui63 flag leaf, score: 94.665 possibly damaging 2 DELETERIOUS 0.00
vg0139276484 G -> A LOC_Os01g67580.1 missense_variant ; p.Ala1337Val; MODERATE nonsynonymous_codon ; A1337V Average:58.831; most accessible tissue: Minghui63 flag leaf, score: 94.665 possibly damaging 1.639 DELETERIOUS 0.00

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0139276484 G A 0.0 0.0 0.0 0.01 0.01 0.01
vg0139276484 G T 0.0 -0.01 -0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0139276484 9.98E-07 9.98E-07 mr1750 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0139276484 1.76E-06 1.76E-06 mr1935 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251